It happened to my Si last week.... Took it to the dealer and they fixed it, they had to take out the whole back seat to fix it.
It seems like the cable release isn't cased so if you have any big stuff or lot of items rolling around inside your trunk, it might get cought on the cable and disconnect it from you latch. Poor design on the trunk latch.

The trunk latch can break with little force and you are locked out. No way to get in with remote of lever without removing the seat. If you have a flat you are out of luck. I am pushing for a recall after spending 200 at dealer on my 2006 Civic EX with 36k miles. I am looking for others with this problem. Please email me with details. Driver beware.